config
¶
Configuration information for PDB2PQR.
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pdb2pqr.config.
AA_DEF_PATH
= 'AA.xml'¶ Expected location for amino acid topology definition file
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pdb2pqr.config.
AA_NAMES
= ['ALA', 'ARG', 'ASH', 'ASN', 'ASP', 'CYS', 'CYM', 'GLN', 'GLU', 'GLH', 'GLY', 'HIS', 'HID', 'HIE', 'HIP', 'HSD', 'HSE', 'HSP', 'ILE', 'LEU', 'LYS', 'LYN', 'MET', 'PHE', 'PRO', 'SER', 'THR', 'TRP', 'TYR', 'TYM', 'VAL']¶ Standard amino acid names
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pdb2pqr.config.
ANGLE_CUTOFF
= 20.0¶ Cutoff for A - D - H(D) hydrogen bond angle
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pdb2pqr.config.
AVOGADRO
= 6.02214076e+23¶ Avogadro’s number
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pdb2pqr.config.
BACKBONE
= ['N', 'CA', 'C', 'O', 'O2', 'HA', 'HN', 'H', 'tN']¶ Standard backbone atom names
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pdb2pqr.config.
BOLTZMANN
= 1.380649e-23¶ Boltzmann constant (in J/K)
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pdb2pqr.config.
BONDED_SS_LIMIT
= 2.5¶ Disulfide bond distance limit
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pdb2pqr.config.
BUMP_HEAVY_SIZE
= 1.0¶ Debumping heavy atom size
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pdb2pqr.config.
BUMP_HYDROGEN_SIZE
= 0.5¶ Debumping hydrogen size
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pdb2pqr.config.
CELL_SIZE
= 2¶ Size of cells used for neighbor lookups
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pdb2pqr.config.
CITATIONS
= ['Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018).', 'Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).']¶ Citation strings for PDB2PQR
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pdb2pqr.config.
DEBUMP_ANGLE_STEPS
= 72¶ Number of angle steps to scan when debumping
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pdb2pqr.config.
DEBUMP_ANGLE_STEP_SIZE
= 5.0¶ Size of debumping step
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pdb2pqr.config.
DEBUMP_ANGLE_TEST_COUNT
= 10¶ Debump angle test
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pdb2pqr.config.
DIHEDRAL_WTF
= 57.2958¶ A number of unknown origin used in dihedral angle calculations
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pdb2pqr.config.
DIST_CUTOFF
= 3.3¶ Cutoff for H(D) to A hydrogen bond distance
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pdb2pqr.config.
ELEC_CHARGE
= 1.602176634e-19¶ Electron charge (in C)
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pdb2pqr.config.
FILTER_WARNINGS
= ['Skipped atom during water optimization', 'The best donorH was not picked', 'Multiple occupancies found']¶ The start of warning strings to be filtered.
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pdb2pqr.config.
FILTER_WARNINGS_LIMIT
= 10¶ Number of times warning string is printed before supressing further output
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pdb2pqr.config.
FORCE_FIELDS
= ['amber', 'charmm', 'parse', 'tyl06', 'peoepb', 'swanson']¶ Standard force field names
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pdb2pqr.config.
HYD_DEF_PATH
= 'HYDROGENS.xml'¶ Expected location for hydrogens topology definition file
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pdb2pqr.config.
NA_DEF_PATH
= 'NA.xml'¶ Expected location for nucleic acid topology definition file
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pdb2pqr.config.
NA_NAMES
= ['A', 'A5', 'A3', 'C', 'C5', 'C3', 'G', 'G5', 'G3', 'T', 'T5', 'T3', 'U', 'U5', 'U3', 'RA', 'RG', 'RC', 'RU', 'DA', 'DG', 'DC', 'DT']¶ Standard nucleic acid names
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pdb2pqr.config.
PATCH_DEF_PATH
= 'PATCHES.xml'¶ Expected location for topology patch definition file
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pdb2pqr.config.
PEPTIDE_DIST
= 1.7¶ Peptide bond distance limit
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pdb2pqr.config.
REPAIR_LIMIT
= 0.1¶ Limit on fraction of molecule missing before giving up on repairs
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pdb2pqr.config.
SMALL_NUMBER
= 1e-07¶ A small number used by some math routines.
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pdb2pqr.config.
TITLE_STR
= 'PDB2PQR v3.4.1: biomolecular structure conversion software.'¶ How to format PDB2PQR title in output
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pdb2pqr.config.
TOPOLOGY_DEF_PATH
= 'TOPOLOGY.xml'¶ Expected location for topology definition file
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pdb2pqr.config.
VACUUM_PERMIT
= 8.8541878128e-12¶ Vacuum permittivity (in F/m)
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pdb2pqr.config.
VERSION
= '3.4.1'¶ PDB2PQR version number.